Contacts of the helix formed by residues 217 - 229 (chain A) in PDB entry 1XGS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ARG 3.9 2.0 + - - -
216A VAL* 1.3 74.1 - - - +
218A GLN* 1.3 61.9 + - - +
220A ARG* 3.3 24.0 + - - +
221A PHE* 2.9 47.1 + - + -
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A VAL* 4.2 6.6 - - + +
217A ALA* 1.3 75.9 - - - +
219A ALA* 1.3 60.9 + - - +
221A PHE* 3.8 22.0 - - - +
222A LEU* 2.8 30.1 + - - +
244A MET* 3.3 31.1 - - + +
248A GLN* 2.9 43.5 - - - +
252A ALA* 4.7 2.9 - - + -
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 3.5 22.7 - - + -
216A VAL* 3.6 12.2 + - + +
217A ALA 3.2 0.4 - - - -
218A GLN* 1.3 76.8 - - - +
220A ARG* 1.3 58.7 + - - +
222A LEU* 3.1 7.2 + - - +
223A LEU* 2.8 30.5 + - - +
252A ALA* 4.0 23.9 - - - +
255A THR* 3.9 20.0 - - + -
256A LEU* 3.7 6.9 - - + +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL* 3.0 41.6 + - + +
215A ARG* 3.2 20.6 + - - +
216A VAL 2.9 17.6 + - - +
217A ALA* 3.6 25.7 - - - +
219A ALA* 1.3 77.8 - - - +
221A PHE* 1.3 60.8 + - + +
223A LEU* 3.5 6.4 + - + +
224A ALA* 3.1 24.4 + - - +
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Residues in contact with PHE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ALA* 2.9 40.2 + - + +
218A GLN* 3.8 21.8 - - - +
220A ARG* 1.3 77.9 - - + +
222A LEU* 1.3 64.4 + - - +
224A ALA* 3.2 10.4 + - + +
225A LYS* 3.0 21.7 + - - +
228A ARG* 4.9 1.9 + - - -
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A GLN* 2.8 20.9 + - - +
219A ALA 3.3 5.8 - - - +
221A PHE* 1.3 75.7 - - - +
223A LEU* 1.3 64.8 + - - +
225A LYS* 3.0 13.7 + - + +
226A ILE* 2.9 30.4 + - + +
240A LEU* 4.0 30.5 - - + -
243A ASP* 5.1 1.1 - - + +
244A MET* 4.0 22.4 - - + -
249A LEU* 4.5 6.1 - - + -
252A ALA* 3.6 26.5 - - + -
253A LEU* 4.2 20.9 - - + +
256A LEU* 4.1 12.8 - - + -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 3.7 31.6 - - + -
211A ASP* 5.0 4.5 - - - +
212A VAL* 4.1 11.4 - - + +
214A VAL* 3.8 23.8 - - + -
219A ALA 2.8 19.1 + - - +
220A ARG* 3.8 7.6 - - + +
222A LEU* 1.3 73.3 - - - +
224A ALA* 1.3 57.0 + - - +
226A ILE* 3.4 6.2 + - + -
227A LYS* 2.9 48.8 + - + +
256A LEU* 3.9 16.1 - - + +
261A ALA* 4.0 21.5 - - + -
262A ILE* 4.4 6.5 - - + -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG 3.1 16.1 + - - +
221A PHE* 3.3 17.3 - - + +
222A LEU 3.1 0.2 - - - -
223A LEU* 1.3 79.1 - - - +
225A LYS* 1.3 56.9 + - - +
227A LYS* 4.0 8.1 - - - +
228A ARG* 3.1 42.7 + - - +
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PHE 3.0 10.7 + - - +
222A LEU* 3.0 14.0 + - + +
224A ALA* 1.3 75.2 - - - +
226A ILE* 1.3 56.7 + - - +
228A ARG* 3.2 27.5 + - - +
229A GLU* 2.7 62.8 + - + +
230A TYR* 4.2 11.7 - - + +
239A TRP 5.3 2.2 - - - -
240A LEU* 3.9 13.9 - - + -
243A ASP* 2.9 39.1 + - - +
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Residues in contact with ILE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 3.8 23.1 - - + -
222A LEU* 2.9 31.8 + - + +
223A LEU* 3.6 9.6 - - + +
225A LYS* 1.3 73.7 - - - +
227A LYS* 1.3 58.3 + - - +
230A TYR* 2.8 45.0 + - + -
231A GLY 3.1 7.0 + - - +
235A PHE* 3.6 51.1 - - + -
240A LEU* 4.9 3.4 - - + -
253A LEU* 5.0 2.2 - - + -
256A LEU* 4.1 24.2 - - + -
262A ILE* 4.3 5.6 - - + -
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 3.7 44.2 - - + +
211A ASP* 3.3 25.0 + - - +
223A LEU* 2.9 37.5 + - + +
224A ALA* 4.0 7.2 - - - +
226A ILE* 1.3 75.4 - - - +
228A ARG* 1.3 61.4 + - - +
231A GLY* 3.5 21.9 + - - +
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LYS* 6.0 0.3 + - - -
221A PHE 4.9 1.8 + - - -
224A ALA* 3.1 38.3 + - - +
225A LYS* 3.4 41.5 + - - +
227A LYS* 1.3 78.5 - - - +
229A GLU* 1.3 69.2 + - + +
231A GLY 4.8 0.2 - - - -
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 4.3 20.4 + - - +
86A HIS* 6.0 0.5 - - - -
225A LYS* 2.7 58.2 + - + +
228A ARG* 1.3 88.0 + - + +
230A TYR* 1.3 86.8 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il